If you're going to insist on "milling" out the chassis (since you're using a dremel by hand, it isn't milling since you aren't using a milling machine), take a look at the Storm Pro chassis, which is milled. The slot locations and the amount of material removed will determine how much weaker you're going to make the chassis. Personally, I'd live with the extra ounce or two. BTW, the Pro chassis does not mount anything lower than on the stock chassis, you want maximum thickness around all areas in which you mount components.

I would buy a storm pro chassis before ruining the stock one.